Research Subject

Comprehensive single cell analyses on developmental transitions and reprogramming events in mammalian pluripotent stem cells

Kuniya Abe

RIKEN BioResource Center
Technology and Development Team for Mammalian Genome Dynamics
Team Leader

〒305-0074 つくば市高野台3−1−1 バイオリソースセンター

“We have been studying mammalian development and stem cells. Currently we focus on peri-implantation embryos and stem cells derived from these embryos, i.e. ES cells and Epiblast stem cells (EpiSC). Mouse ES (mES) cells are known as “”naïve”” type stem cells, whereas EpiSCs belong to “”primed”” type stem cells. These two types of stem cells show distinct epigenetic states, as exemplified by differences in their global DNA methylation patterns, X chromosome inactivation (XCI) status, and other mono-allelic gene expression including imprinted genes, and it is considered that “”epigenetic barrier”” exists between the two stem cell types. Naive-primed conversion is associated with significant changes in transcriptional and epigenetic networks, and cell-cell interactions must play important roles in this transition. However, it is largely unknown which factors or genes are important for this transition process.

We recently published novel method for efficient derivation of high quality EpiSCs using Wnt inhibitor (Stem Cell Reports, 2015). Using similar culture condition, we could establish very efficient cell differentiation protocol from mESC to EpiSCs. Unlike the other existing protocol, cell death or spontaneous differentiation to somatic cells are hardly seen in this system. In female cells, random X chromosome inactivation occurs synchronously in >90% of cells, representing extremely useful in vitro model for XCI studies.

Single-cell multi-omics analyses of naive-primed conversion process are currently ongoing: Using the ES-EpiSC differentiation system described above, the “”real”” molecular events underlying the stem cell differentiation process will be delineated in detail. In addition to single cell RNA-Seq analysis, single cell-CAGE analysis is also being performed. The CAGE analysis will reveal the enhancer/promoter interplay, the lncRNAs at imprinted loci, and allelic exclusions, which will help us to learn about the series of events that drive genome hierarchical regulation during development.

Comprehensive analyses on transition process from naïve-to-primed pluripotent state